Solid-state 13C NMR detection of a perturbed 6-s-trans chromophore in bacteriorhodopsin

Solid-state 13C magic angle sample spinning NMR spectroscopy has been used to study the ionone ring portion of the chromophore of bacteriorhodopsin. Spectra were obtained from fully hydrated samples regenerated with retinals 13C labeled at positions C-5, C-6, C-7, C-8, and C-18 and from lyophilized samples regenerated with retinals labeled at C-9 and C-13. C-15-labeled samples were studied in both lyophilized and hydrated forms. Three independent NMR parameters (the downfield element of the C-5 chemical shift tensor, the C-8 isotropic chemical shift, and the C-18 longitudinal relaxation time) indicate that the chromophore has a 6-s-trans conformation in the protein, in contrast to the 6-s-cis conformation that is energetically favored for retinoids in solution. We also observe an additional 27 ppm downfield shift in the middle element of the C-5 shift tensor, which provides support for the existence of a negatively charged protein residue near C-5. Evidence for a positive charge near C-7, possibly the counterion for the negative charge, is also discussed. On the basis of these results, we present a new model for the retinal binding site, which has important implications for the mechanism of the "opsin shift" observed in bacteriorhodopsin.     

Characterisation of Schiff base and chromophore in green proteorhodopsin by solid-state NMR

The proteorhodopsin family consists of hundreds of homologous retinal containing membrane proteins found in bacteria in the photic zone of the oceans. They are colour tuned to their environment and act as light-driven proton pumps with a potential energetic and regulatory function. Precise structural details are still unknown. Here, the green proteorhodopsin variant has been selected for a chemical shift analysis of retinal and Schiff base by solid-state NMR. Our data show that the chromophore exists in mainly all-trans configuration in the proteorhodopsin ground state. The optical absorption maximum together with retinal and Schiff base chemical shifts indicate a strong interaction network between chromophore and opsin. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Mark Lorch and Andreas C. Woerner contributed equally to this work.     

Molecular dynamics study of the M412 intermediate of bacteriorhodopsin.

Molecular dynamics simulations have been carried out to study the M412 intermediate of bacteriorhodopsin's (bR) photocycle. The simulations start from two simulated structures for the L550 intermediate of the photocycle, one involving a 13-cis retinal with strong torsions, the other a 13,14-dicis retinal, from which the M412 intermediate is initiated through proton transfer to Asp-85. The simulations are based on a refined structure of bR568 obtained through all-atom molecular dynamics simulations and placement of 16 waters inside the protein. The structures of the L550 intermediates were obtained through simulated photoisomerization and subsequent molecular dynamics, and simulated annealing. Our simulations reveal that the M412 intermediate actually comprises a series of conformations involving 1) a motion of retinal; 2) protein conformational changes; and 3) diffusion and reconfiguration of water in the space between the retinal Schiff base nitrogen and the Asp-96 side group. (1) turns the retinal Schiff base nitrogen from an early orientation toward Asp-85 to a late orientation toward Asp-96; (2) disconnects the hydrogen bond network between retinal and Asp-85 and tilts the helix F of bR, enlarging bR's cytoplasmic channel; (3) adds two water molecules to the three water molecules existing in the cytoplasmic channel at the bR568 stage and forms a proton conduction pathway. The conformational change (2) of the protein involves a 60 degrees bent of the cytoplasmic side of helix F and is induced through a break of a hydrogen bond between Tyr-185 and a water-side group complex in the counterion region.     

15N and 13C NMR studies of ligands bound to the 280,000-dalton protein porphobilinogen synthase elucidate the structures of enzyme-bound product and a Schiff base intermediate

Porphobilinogen synthase (PBGS) catalyzes the asymmetric condensation of two molecules of 5-aminolevulinic acid (ALA). Despite the 280,000-dalton size of PBGS, much can be learned about the reaction mechanism through 13C and 15N NMR. To our knowledge, these studies represent the largest protein complex for which individual nuclei have been characterized by 13C or 15N NMR. Here we extend our 13C NMR studies to PBGS complexes with [3,3-2H2,3-13C]ALA and report 15N NMR studies of [15N]ALA bound to PBGS. As in our previous 13C NMR studies, observation of enzyme-bound 15N-labeled species was facilitated by deuteration at nitrogens that are attached to slowly exchanging hydrogens. For holo-PBGS at neutral pH, the NMR spectra reflect the structure of the enzyme-bound product porphobilinogen (PBG), whose chemical shifts are uniformly consistent with deprotonation of the amino group whose solution pKa is 11. Despite this local environment, the protons of the amino group are in rapid exchange with solvent (kexchange greater than 10(2) s-1). For methyl methanethiosulfonate (MMTS) modified PBGS, the NMR spectra reflect the chemistry of an enzyme-bound Schiff base intermediate that is formed between C4 of ALA and an active-site lysine. The 13C chemical shift of [3,3-2H2,3-13C]ALA confirms that the Schiff base is an imine of E stereochemistry. By comparison to model imines formed between [15N]ALA and hydrazine or hydroxylamine, the 15N chemical shift of the enzyme-bound Schiff base suggests that the free amino group is an environment resembling partial deprotonation; again the protons are in rapid exchange with solvent. Deprotonation of the amino group would facilitate formation of a Schiff base between the amino group of the enzyme-bound Schiff base and C4 of the second ALA substrate. This is the first evidence supporting carbon-nitrogen bond formation as the initial site of interaction between the two substrate molecules.     

zFP538, a yellow-fluorescent protein from Zoanthus, contains a novel three-ring chromophore

Crystal structures of the tetrameric yellow-fluorescent protein zFP538 from the button polyp Zoanthus sp. and a green-emitting mutant (K66M) are presented. The atomic models have been refined at 2.7 and 2.5 A resolution, with final crystallographic R factors of 0.206 (R(free) = 0.255) and 0.190 (R(free) = 0.295), respectively, and have excellent stereochemistry. The fold of the protomer is very similar to that of green (GFP) and red (DsRed) fluorescent proteins; however, evidence from crystallography and mass spectrometry suggests that zFP538 contains a three-ring chromophore derived from that of GFP. The yellow-emitting species (lambda(em)(max) = 538 nm) is proposed to result from a transimination reaction in which a transiently appearing DsRed-like acylimine is attacked by the terminal amino group of lysine 66 to form a new six-membered ring, cleaving the polypeptide backbone at the 65-66 position. This extends the chromophore conjugation by an additional double bond compared to GFP, lowering the absorption and emission frequencies. Substitution of lysine 66 with aspartate or glutamate partially converts zFP538 into a red-fluorescent protein, providing additional support for an acylimine intermediate. The diverse and unexpected roles of the side chain at position 66 give new insight into the chemistry of chromophore maturation in the extended family of GFP-like proteins.     

Radioimmunoassay of 13, 14-dihydro-15-keto-prostaglandin F2alpha

A simple method is described for the determination of 13, 14-dihydro-15-keto-prostaglandin F2alpha (PGFM), using a highly specific antiserum raised in New Zealand rabbits. It involves extraction of human peripheral venous plasma with diethyl ether after addition of tritiated PGFM and HCl. Radioimmunoassay is performed on appropriate aliquots; after 2 hours or overnight equilibration the bound and free metabolite are separated using dextran-coated charcoal. The mean values +/- S.D. obtained are as follows: healthy males 32 +/- 16 pg/ml, females during follicular phase 48 +/- 18 pg/ml, luteal phase 37 +/- 8 pg/ml, first trimester of pregnancy 66 +/- 33 pg/ml, second trimester 67 +/- 42 pg/ml and third trimester 72 +/- 26 pg/ml.     

Non-random participation of chromosomes 13, 14 and 15 in acrocentric associations

Summary The patterns of association of chromosomes 13, 14 and 15 have been examined in a sample of 23 normal individuals. Significant deviations from the expectation of equality of participation have been detected in many of the individuals studied. The implications of the findings in terms of the aetiology of chromosome abnormality in the D group have been discussed.     

Evidence that MutY is a monofunctional glycosylase capable of forming a covalent Schiff base intermediate with substrate DNA.

The Escherichia coli adenine glycosylase MutY is involved in the repair of 7,8-dihydro-8-oxo-2'-deoxyguanosine (OG):A and G:A mispairs in DNA. DNA strand cleavage via beta-elimination (beta-lyase) activity coupled with MutY's removal of misincorporated adenine bases was sought using both qualitative and quantitative methods. The qualitative assays demonstrate formation of a Schiff base intermediate which is characteristic of DNA glycosylases catalyzing a concomitant beta-lyase reaction. Borohydride reduction of the Schiff base results in the formation of a covalent DNA-MutY adduct which is easily detected in SDS-PAGE experiments. However, quantitative activity assays which monitor DNA strand scission accompanying base release suggest MutY behaves as a simple monofunctional glycosylase. Treatment with base effects DNA strand cleavage at apurinic/apyrimidinic (AP) sites arising via simple glycosylase activity. The amount of cleaved DNA in MutY reactions treated with base is much greater than that in non-base treated reactions, indicating that AP site generation by MutY is not associated with a concomitant beta-lyase step. As standards, identical assays were performed with a known monofunctional enzyme (uracil DNA glycosylase) and a known bifunctional glycosylase/lyase (FPG), the results of which were used in comparison with those of the MutY experiments. The apparent inconsistency between the data obtained for MutY by the qualitative and quantitative methods underscores the current debate surrounding the catalytic activity of this enzyme, and a detailed explanation of this controversy is proposed. The work presented here lays ground for the identification of specific active site residues responsible for the chemical mechanism of MutY enzyme catalysis.     

Evidence for light-induced 13-cis, 14-s-cis isomerization in bacteriorhodopsin obtained by FTIR difference spectroscopy using isotopically labelled retinals

We have obtained by Fourier transformed infra-red (FTIR)-spectroscopy BR-K, BR-L and BR-M difference spectra of bacteriorhodopsin regenerated with isotopically labelled retinals. Thereby, we are able to assign reliably the C₁₄–C₁₅ and C=N stretching vibrations of the various intermediates. The lower C₁₄–C₁₅ stretching vibration frequency in L as compared with 13-cis protonated Schiff base model compounds indicates a 13-cis, 14-s-cis configuration of the retinal in this species. The unusually low C=N stretching vibration in K at 1615 cm⁻¹ indicates less stabilization of the positive charge at the Schiff base by the protein environment. Based on these results, a mechanism is suggested by which the stored light energy is transformed into proton transfers.     

Formation of a Schiff base intermediate is not required for the adenine glycosylase activity of Escherichia coli MutY

The mutY gene product of Escherichia coli is a 39-kDa protein that catalyzes the removal of adenine bases mispaired with 2'-deoxyguanosine and 7,8-dihydro-8-oxo-2'-deoxyguanosine (OG) in DNA. Although adenine removal proceeds via monofunctional glycosylase activity, MutY is able to form covalent adducts with substrate DNA in the presence of borohydride, a trait otherwise known to be associated only with enzymes having bifunctional glycosylase/AP lyase activity. To help identify active site residues involved in the formation of MutY-DNA adducts in the presence of borohydride, a series of site-directed mutant forms of MutY were generated. Our data show that Lys 142 is the primary residue involved in cross-link formation. The absence of Lys 142 results in near elimination of the enzyme-DNA adducts formed relative to wild-type, suggesting that this residue is the primary one involved in forming covalent associations with DNA during MutY catalysis. Importantly, the enzymatic activity and DNA binding of the K142A enzyme is nearly identical to the WT enzyme. This shows that formation of the covalent intermediate is not required for adenine removal by MutY. Furthermore, this suggests that the covalent intermediate is formed by reaction of Lys 142 with the OG/G:(AP site) product, and this may be a consequence of MutY's unusually high affinity for the product of its glycosylase action.     

Radioimmunoassay of 13, 14-dihydro-15-keto-prostaglandin F2a

A simple method is described for the determination of 13, 14-dihydro-15-keto-prostaglandin F_2a, (PGFM), using a highly specific antiserum raised in New Zealand rabbits. It involves extraction of human peripheral venous plasma with diethyl ether after addition of tritiated PGFM and HCl. Radioimmunoassay is performed on appropriate aliquots; after 2 hours or overnight equilibration the bound and free metabolite are separated using dextran-coated charcoal. The mean values ± S.D. obtained are as follows: healthy males 32 ± 16 pg/ml, females during follicular phase 48 ± 18 pg/ml, luteal phase 37 ± 8 pg/ml, first trimester of pregnancy 66 ± 33 pg/ml, second trimester 67 ± 42 pg/ml and third trimester 72 ± 26 pg/ml.     

Effect of iodination on the pK of Schiff base deprotonation and M412 production in purple membrane

Previously, kinetic resonance Raman measurements as a function of pH have been used to demonstrate that, microseconds after light absorption, the pK of Schiff base deprotonation during the bacteriorhodopsin photocycle is 10.2 ± 0.3, whereas before the light event, the pK is > 12 (2). In this investigation, we have iodinated purple membrane suspensions and have found that the pK of Schiff base deprotonation in the photocycle has been lowered to between 7 and 8 for iodinated bacteriorhodopsin. These results, together with our previous data on the pK of Schiff base deprotonation, suggest that the amino acid tyrosine could be a critical component in the deprotonation mechanism.     

Radioimmunoassay of 13, 14-dihydro-15-keto prostaglandin F in bovine peripheral plasma.

A radioimmunoassay has been developed for 13, 14-dihydro-15-keto-prostaglandin F in bovine peripheral plasma. Acidified plasma samples were extracted with diethyl ether and the dried extract assayed for 13, 14-dihydro-15-keto-prostaglandin F using antiserum raised against a 13, 14-dihydro-15-keto-prostaglandin F2alpha-albumin complex. The tracer used for the assay was prepared enzymatically from tritiated prostaglandin F1alpha. Polyethylene glycol was employed to separate free and bound 13, 14-dihydro-15-keto-prostaglandin F. The inter-assay coefficient of variation based on 9 determinations of control plasma was 13.8%. The detection limit of the assay was 25 pg 13, 14-dihydro-15-keto-prostaglandin F/ml plasma. In 3 cows around estrus there was a complex sseries of peaks of 13, 14-dihydro-15-keto-prostaglandin F concentrations coincident with luteolysis and declining progesterone concentrations. Changes in peripheral plasma concentrations of 13, 14-dihydro-15-keto-prostaglandin F in the pregnant cow near term showed a close correlation with prostaglandin F levels in utero-ovarian venous plasma. The concentration of 13, 14-dihydro-15-keto-prostaglandin F in 12 men was 114 +/- 20 pg/ml plasma. It is concluded that the measurement of peripheral 13, 14-dihydro-15-keto-prostaglandin F concentrations may offer a simple and convenient method for monitoring uterine prostaglandin F production in the cow.     

1H, 15N, 13C and 13CO resonance assignments and secondary structure of villin 14T,a domain conserved among actin-severing proteins

Summary Sequence-specific assignments have been made for the ¹H, ¹⁵N, ¹³C and ¹³CO resonances of 14T, the 126-residue amino-terminal domain of the actin-severing protein villin. Villin is a member of a family of proteins that regulate cytoskeletal actin by severing, capping and nucleating actin filaments. Actin binding is dependent on calcium and disrupted by phosphatidyl inositol 4,5-bisphosphate. Actin-severing proteins are built from three or six repeats of a conserved domain, represented by 14T. Expression in Escherichia coli facilitated incorporation of ¹⁵N and ¹³C isotopes and application of triple-resonance, backbone-directed strategies for the sequential assignments. Elements of regular secondary structure have been identified by characteristic patterns of NOE cross peaks and values of vicinal ³J_H n _H coupling constants. Amide protons that exchange slowly (rates less than 1.0×10^-4 per min) are concentrated in the central -sheet and the second and third -helices, suggesting that these elements of secondary structure form very stable hydrogen bonds. Assignments for the amide nitrogens and protons have been examined as a function of pH and calcium concentration. Based on the conservation of chemical shifts in the core of the domain, villin 14T maintains the same overall fold in the pH range from 4.15 to 6.91 and the calcium range from 0 to 50 mM. The calcium data indicate the presence of two calcium-binding sites and suggest their locations.     

Synthesis, crystal structure and electroluminescent properties of a Schiff base zinc complex

A new complex of zinc with a Schiff base, zinc(N,N′-bis(salicylidene)-3, 6-dioxa-1, 8-diaminooctane monohydrate) (ZnBSO · H₂O), was synthesized and characterized by means of elemental analyses, IR spectra and DTA-TG. Its structure was determined by X-ray single crystal analysis. It was demonstrated that the zinc atom is coordinated by the two oxygen atoms in phenolate and two nitrogen atoms in imine of the ligand in a slightly distorted tetrahedral geometry, while the two oxygen atoms from the oxa-alkyl chain are not coordinated to Zn(II) atom. The energy levels of the HOMO, LUMO and the electrochemical band gap were determined by cyclic voltammeter. The electroluminescent devices with the complex as the emitter showed bright blue emission with a peak at 450 nm, which is same as the fluorescence of the complex in both solution and solid states.     

Preparation and Metabolism of 2-(14C)-cis, trans-Xanthoxin

2-[¹⁴C]-cis, trans-xanthoxin (specific activity 0.26 µCi/µmol)has been synthesized from4-(1', 2'-epoxy-4'-hydroxy-2', 6',6'-trimethyl-l'-cyclohexyl)-trans-3-buten-2-oneand methyl 2-[¹⁴C]-bromoacetate. When 2-[¹⁴C]-cis, trans-xanthoxin was fed to cut shoots of tomatoand dwarf bean, it was converted within 8 h to (+)-abscisicacid in yields of 10.8 and 7.0 per cent respectively. Pea seedsand tomato fruits gave much smaller conversions. A second majormetabolic product extracted from treated tomato and bean shootswas shown to be a metabolite of abscisic acid and has been tentativelyidentified as phaseic acid. These results, together with the earlier finding that xanthoxinis present in the extracts of many seedlings, suggest that xanthophyllsand xanthoxin may be precursors in the biosynthesis of ( + )-abscisicacid